Search Results (46)

Waardenburg syndrome (WS) represents a group of genetic conditions characterized by auditory and pigmentation defects. Pathogenic variants in PAX3, MITF, SOX10, EDN3, EDNRB, SNAI2, and KITLG genes have been associated with WS across multiple populations; a comprehensive study of WS in Africa has not yet been reported. We conducted a systematic review of clinical expressions and genetics of WS across Africa. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines were followed, and the study protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews (2025 CRD420250655744). A literature search was performed on Google Scholar, PubMed, Scopus, Directory of Open Access Journals (DOAJ), Global Index Medicus, African-Wide Information, ScienceDirect, Connecting Repositories (CORE), and the Web of Science databases. We reviewed a total of 15 articles describing 84 WS cases, which showed no gender bias and a mean age at reporting of 17.5 years. Congenital, sensorineural, and profound hearing loss was described in most cases (66.7%; n = 56/84). WS type 2 (WS2), with characteristically no dystopia canthorum, is the predominant subtype (36.9%; n = 31/84). Pathogenic variants in four WS known genes, i.e., PAX3 (13 families), SOX10 (7 families), EDNRB (4 families), and EDN3 (1 family), were reported in Morocco, Tunisia, and South Africa. One candidate gene (PAX8) was described in one family in Ghana. Two non-syndromic hearing loss (NSHL) genes (BDP1 and MYO6) were reported in two separate families in South Africa, suggesting a possible phenotypic expansion. The highest number of WS cases was described in South Africa (38.1%; n = 32/84) and Tunisia (26.2%; n = 22/84). Gene variants were missense (27/43), deletion (7/43), splicing (5/43), nonsense (2/43), indel (1/43), and duplication (1/43), chiefly segregating in an autosomal dominant inheritance mode. There was no functional data to support the pathogenicity of putative causative variants. This review showed that WS2 is the most common in Africa. Variants in PAX3 and SOX10 were the predominant genetic causes. This study emphasizes the need to further investigate in-depth clinical characterization, molecular landscape, and the pathobiology of WS in Africa. Full article

Coral reefs, with their high biodiversity and ecological service functions, face significant threats due to climate change, overfishing, and pollution. The South China Sea (SCS) hosts rich coral biodiversity, particularly Acropora hyacinthus, a critical species for reef restoration. However, the region’s coral reefs are increasingly degraded, highlighting the urgent need for conservation efforts. In the present study, the genetic diversity and population structure of A. hyacinthus were examined based on two types of data: double-digest restriction-site-associated DNA (ddRAD) sequencing data and mitochondrial putative control region DNA (mtCR) sequences. Coral tissue samples were collected from 74 colonies inhabiting two inshore reefs (Sanya) and three offshore reefs (Xisha islands), and 748 single nucleotide polymorphisms (SNPs) and 74 mtCR sequences were obtained and utilized for downstream analysis. The results were consistent in analyses and did not cluster into two geographical groups for the inshore and offshore sites. Phylogenetic analysis showed that individuals of A. hyacinthus inhabiting the five detected sites were likely cryptic species HyaD. Furthermore, AMOVA and pairwise F_ST estimations based on both data types revealed no differentiation among five populations and between inshore and offshore reefs, which could be due to the reproductive mode of broadcast spawning for this species. However, a prevalent low level of genetic diversity was observed when compared with nearby Taiwan regions and Japan, and the geographic history results showed that the effective population size (N_e) had been decreasing for the past 300 years. Thus, we speculated that the populations of A. hyacinthus inhabiting the SCS lack the potential to cope with future climate change adequately, and multiple conservation measures should be implemented based on considering genetic diversity. Full article

Parasites of the Leishmania genus are globally distributed and cause various clinical presentations in animals and humans, collectively known as leishmaniasis. The genomes of Leishmania and other trypanosomatids exhibit remarkable plasticity, shaped by several distinctive genetic features. Although these features can hinder the application of next-generation DNA sequencing (NGS) technologies, NGS data have been successfully used to characterize the whole-genome diversity of circulating Leishmania strains. The results complement and are broadly aligned with previous findings obtained with more traditional methods, offering greater resolution when working with geographically closer strains. In this review, we summarize advances over the past two decades in characterizing the genome diversity of Leishmania parasites using NGS strategies. We also discuss the application of these strategies to elucidate other aspects relevant to the epidemiology of these parasites, including their population structure and mode of reproduction. The vast majority of the studies to date have focused on species within the L. donovani/infantum complex or the L. (Viannia) subgenus, highlighting the need to incorporate other relevant underrepresented species and regions from both the Old and New World. Full article

1,3-butadiene (BD) is a volatile organic pollutant. Upon inhalation, it is metabolically activated to reactive epoxides which alkylate genomic DNA and form potentially mutagenic monoadducts and DNA–DNA crosslinks including N7-(1-hydroxyl-3-buten-1-yl)guanine (EB-GII) and 1,4-bis-(guan-7-yl)-2,3-butanediol (bis-N7G-BD). While metabolic activation resulting in mutagenicity is a well-established mode of action for 1,3-butadiene, characterization of the extent of inter-individual variability in response to BD exposure is a gap in our knowledge. Previous studies showed that population-wide mouse models can be used to evaluate variability in 1,3-butadiene DNA adducts; therefore, we hypothesized that this approach can be used to also study variability in the formation and loss of BD DNA adducts across tissues and between sexes. To test this hypothesis, female and male mice from five genetically diverse Collaborative Cross (CC) strains were exposed to filtered air or 1,3-butadiene (600 ppm, 6 h/day, 5 days/week for 2 weeks) by inhalation. Some animals were kept for two additional weeks after exposure to study DNA adduct persistence. EB-GII and bis-N7G-BD adducts were quantified in liver, lungs and kidney using established isotope dilution ESI-MS/MS methods. We observed strain- and sex-specific effects on both the accumulation and loss of both DNA adducts, indicating that both factors play important roles in the mutagenicity of 1,3-butadiene. In addition, we quantified the intra-species variability for each adduct and found that for most tissues/adducts, variability values across strains were modest compared to default uncertainty factors. Full article

Citrus tristeza virus (CTV) is an important pathogen threatening the global citrus industry, but its evolution and transmission mechanism in wild citrus has not been clarified. Most of the existing studies are based on CTV-specific gene fragments, lacking genome-wide analysis. There is especially a lack of understanding of CTV transmission dynamics in wild citrus, which needs further investigation. In this study, wild citrus samples from three provinces of China were collected, virus genome data were obtained by high-throughput sequencing (HTS) technology and combined with public database data, and Bayesian phylogeographic inference was used to analyze virus composition characteristics in wild citrus, as well as the population genetic structure, temporal dynamic evolution, and spatial transmission mode of CTV. The results showed that Yunnan wild citrus samples contained the most abundant virus components, including CTV, Citrus Exocortis Viroid (CEVd), Citrus associated Ampelovirus 1 (CaAV-1), and Citrus Virus B (CiVB), while Jiangxi and Hunan samples only contained CTV and CEVd, with all samples showing mixed infection. Phylogenetic analysis showed that nine wild citrus CTV isolates were scattered in different evolutionary clades, and only 9.27% of genetic variation existed between the populations, while 90.72% of genetic variation existed within the populations, indicating little effect of geographic isolation on gene flow. The time to the most recent common ancestor (tMRCA) of CTV was estimated at 1360 CE, with subsequent divergence into two lineages, with population size stabilizing after a rapid increase in 1980–1990. Asia has been identified as the central source of CTV’s global spread, with key migration events including Asia to North America (1746), Asia to Oceania (1829), and Asia to South America (1965), coinciding with global maritime trade and the expansion of the citrus industry. Full article

The study examined the association between body composition and beverage consumption and the risk of asthma and chronic obstructive pulmonary disease (COPD) and explored the single nucleotide polymorphisms (SNPs) involved in these associations by leveraging summary statistics from genome-wide association studies (GWAS) in nonoverlapping populations. The IEU OpenGWAS project was sourced for exposure datasets: body mass index, body fat percentage, fat-free mass, total body water mass, alcohol intake frequency, and coffee intake, and selected health outcome datasets: asthma and chronic obstructive pulmonary disease. Datasets were assessed and filtered using R, followed by a two-sample Mendelian randomization analysis. The MR Egger, weighted median, inverse variance weighted, simple mode, and weighted mode methods were used to examine the association between exposures and outcomes. Heterogeneity and pleiotropy analyses were used to evaluate the reliability of results. Additionally, SNPnexus was used to ascertain SNPs linked to established phenotypes, while SNP annotation was obtained from the Ensembl BioMart database via the biomaRt package. Genes belonging to overlapping groups were visualized using ComplexHeatmap. Higher body fat percentage (OR = 1.72, 95% CI: 1.23–2.41, p = 0.002), increased BMI (OR = 1.56, CI: 1.23–1.20, p = 2.53 × 10⁻⁴), and more frequent alcohol intake (OR = 1.34, CI: 1.08–1.68, p = 0.009) were associated with elevated COPD risk. Asthma risk was similarly increased with higher body fat percentage (OR = 1.60, CI: 1.23–2.21, p = 0.001), BMI (OR = 1.54, CI: 1.29–1.84, p = 2.23 × 10⁻⁶), fat-free mass (OR = 1.21, CI: 1.02–1.44, p = 0.032), and alcohol intake frequency (OR = 1.19, CI: 1.01–1.40, p = 0.039). Total body water mass and coffee intake were not associated with asthma and COPD. SNP annotation revealed that some genetic variants that influenced the association of the exposure variables with asthma and COPD were missense variants in several genes, including the evolutionarily highly conserved gene, SLC39A8 (rs13107325; C/A/T allele), and POC5 (rs2307111; T/A/C allele), as well as intronic variants in FTO (rs56094641; A/G/T allele) and NRXN3 (rs10146997; A/G allele). The discovery of the missense variants rs13107325 and rs2307111 in SLC39A8 and POC5, respectively, in addition to other intronic and synonymous SNPs suggests that these SNPs may have some roles in the development or progression of asthma and COPD. This may contribute to the identification of molecular signatures or biomarkers that forecast the risk, development, or therapeutic response of chronic lung diseases in persons with metabolic dysregulation, including obesity. Full article

This research evaluates the performance of six metaheuristic algorithms in the active and reactive power management of wind turbines (WTs) integrated into an AC microgrid (MG). The population-based genetic algorithm (PGA) is proposed as the primary optimization strategy and is rigorously compared against five benchmark techniques: Monte Carlo (MC), particle swarm optimization (PSO), the JAYA algorithm, the generalized normal distribution optimizer (GNDO), and the multiverse optimizer (MVO). This study aims to minimize, through independent optimization scenarios, the operating costs, power losses, or CO₂ emissions of the microgrid during both grid-connected and islanded modes. To achieve this, a coordinated control strategy for distributed generators is proposed, offering flexible adaptation to economic, technical, or environmental priorities while accounting for the variability of power generation and demand. The proposed optimization model includes active and reactive power constraints for both conventional generators and WTs, along with technical and regulatory limits imposed on the MG, such as current thresholds and nodal voltage boundaries. To validate the proposed strategy, two scenarios are considered: one involving 33 nodes and another one featuring 69. These configurations allow evaluation of the aforementioned optimization strategies under different energy conditions while incorporating the power generation and demand variability corresponding to a specific region of Colombia. The analysis covers two-time horizons (a representative day of operation and a full week) in order to capture both short-term and weekly fluctuations. The variability is modeled via an artificial neural network to forecast renewable generation and demand. Each optimization method undergoes a statistical evaluation based on multiple independent executions, allowing for a comprehensive assessment of its effectiveness in terms of solution quality, average performance, repeatability, and computation time. The proposed methodology exhibits the best performance for the three objectives, with excellent repeatability and computational efficiency across varying microgrid sizes and energy behavior scenarios. Full article

Lactarius hatsudake is an economically important wild edible fungus in sub-tropical and temperate Asia. At present, little is known about its genetic diversity, mode of reproduction, and population structure in natural environments. In this study, we collected 102 specimens from eight geographic locations across three provinces in southwest China. Five simple sequence repeat markers that demonstrated high polymorphism were developed and used to analyze the patterns of genetic variations within and among the eight geographic populations. Analyses of molecular variance revealed that 60% of the observed genetic variation occurred among populations, with the remaining 40% attributable to within populations, while inter-provincial variation was nonsignificant. Combined analyses based on discriminant analysis of principal components, STRUCTURE, and the unweighted pair group method with arithmetic mean identified two distinct genetic subpopulations with each genetic subpopulation showing a wide geographical distribution, a result consistent with ancient divergence and recent gene flow within this species in southwest China. Interestingly, excess homozygosity was observed at most loci in almost all of the eight geographic populations, consistent with inbreeding being common for this species in nature. Together, our results revealed the genetic diversity, mode of reproduction, and geographic structuring of this important wild mushroom in southwest China. Full article

The Japanese archipelago as a continental island of the Eurasia continent and harboring high levels of plant species diversity provides an ideal geographical setting for investigating vicariant allopatric speciation due to the sea-level fluctuations associated with climatic oscillations during the Quaternary. In this study, three chloroplast DNA regions and 14 nuclear loci were sequenced for 31 individuals from three populations of Torreya nucifera var. nucifera and 52 individuals from three populations of T. nucifera var. radicans. Population genetic analyses (Network, STRUCTURE and phylogeny) revealed that the genetic boundaries of the two varieties are distinct, with high genetic differentiation (F_ST) of 0.9619 in chloroplast DNA and 0.6543 in nuclear loci. The relatively ancient divergence times between the two varieties were estimated to 3.03 Ma by DIYABC and 1.77 Ma by IMa2 when dated back to the late Pliocene and the early Pleistocene, respectively. The extremely weak gene flow (2Nm = 0.1) between the two varieties was detected by IMa2, which might be caused by their population expansion since the early Pleistocene (~2.0 Ma) inferred in the Bayesian skyline plots and DIYABC. Niche modeling showed that the two varieties had significant ecological differentiation (p < 0.001) since the Last Interglacial even earlier. These results demonstrate that vicariant allopatric speciation due to sea-level fluctuations may be a common mode of speciation in the Japanese archipelago. This finding provides insights into the understanding of species diversification in the Japanese Archipelago and even East Asian flora under climatic oscillations during the Quaternary. Full article

The species of the genus Rhynchium Spinola are important natural insect control resources and widespread in the Old World. Due to the various color patterns of several species in China, it is difficulty to accurately classify and identify the genus. We combined their morphology with population genetic differentiation, phylogenetic relationship and geographical distribution to delimitate the species of Rhynchium from China. Within the genus, more than 600 pinned specimens were examined and a total of 37 whole genomes were analyzed, of which 35 were newly sequenced. Firstly, COI sequences, 13 PCGs and 2 rRNAs sequences of the mitochondrial genomes, USCO nucleotide matrix of 90% completeness (USCO90_fna), and USCO amino acid matrix of 90% completeness (USCO90_faa) were extracted from the whole-genome data. Then, genetic distances were calculated using the COI sequences, and ABGD species delimitation analysis identified three valid species. By integrating the four phylogenetic trees inferred from the four datasets and morphological analysis, the specimens of Rhynchium from China were recognized as R. carnaticum (newly recorded), R. quinquecinctum, and R. brunneum; the last is the most widely distributed in China, while the remaining two only occur in Hainan and Yunnan, respectively, markedly different from previous records. Finally, it is interesting that color patterns of the species R. brunneum seem to closely relate to the geographical distribution, embodying two different modes in the South and the North of China, as well as a transitional state in the middle. The roles of the color patterns are still not resolved and their underlying evolutionary mechanisms need further exploration. Full article

Pleurotus tuoliensis is a unique species discovered in Xinjiang, China, which is recognized for its significant edible, medicinal, and economic value. It has been successfully incorporated into industrial production. Controversy has emerged concerning the evolution and environmental adaptability of this species due to inadequate interspecific ecology and molecular data. This study examines the germplasm resources of P. tuoliensis in the Xinjiang region. A total of 225 wild and cultivated strains of P. tuoliensis were gathered from seven representative regions. Phylogenetic analysis revealed that seven populations were notably segregated into three distinct groups, primarily attributed to environmental factors as the underlying cause for this differentiation. Population historical size data indicate that P. tuoliensis underwent two expansion events, one between 2 and 0.9 Mya (Miocene) and the other between 15 and 4 Mya (Early Pleistocene). The ancient climate fluctuations in the Xinjiang region might have contributed to the comparatively modest population size during the Pliocene epoch. Moreover, through the integration of biogeography and ancestral state reconstruction, it was determined that group C of P. tuoliensis emerged initially and subsequently dispersed to groups D and B, in that order. Subsequently, group D underwent independent evolution, whereas group B continued to diversify into groups A and EFG. The primary factor influencing this mode of transmission route is related to the geographical conditions and prevailing wind direction of each group. Subsequent research endeavors focused on assessing the domestication adaptability of P. tuoliensis to different substrates. It was found that the metabolic processes adapted during the domestication process were mainly related to energy metabolism, DNA repair, and environmental adaptability. Processes adapted to the host adaptability include responses to the host (meiosis, cell cycle, etc.) and stress in the growth environment (cysteine and methionine metabolism, sulfur metabolism, etc.). This study analyzed the systematic evolution and genetic differentiation of P. tuoliensis in Xinjiang. The identified loci and genes provide a theoretical basis for the subsequent improvement of germplasm resources and conducting molecular breeding. Full article

Background: Sensorineural hearing loss (SNHL) is a multifactorial disorder with potential links to various physiological systems, including the cardiovascular system via blood lipid levels such as triglycerides (TG). This study investigates the causal relationship between TG levels and SNHL using Mendelian randomization (MR), which offers a method to reduce confounding and reverse causality by using genetic variants as instrumental variables. Methods: Utilizing publicly available genome-wide association study (GWAS) data, we performed a two-sample MR analysis. The initial analysis unveiled a causal relationship between TG (GWAS ID: ebi-a-GCST90018975) and SNHL (GWAS ID: finn b-H8_HL_SEN-NAS). Subsequent analysis validated this through MR with a larger sample size for TG (GWAS ID: ieu-b-111) and SNHL. To conduct the MR analysis, we utilized several methods including inverse-variance weighted (IVW), MR Egger, weighted median, and weighted mode. We also employed Cochrane’s Q test to identify any heterogeneity in the MR results. To detect horizontal pleiotropy, we conducted the MR-Egger intercept test and MR pleiotropy residual sum and outliers (MR-PRESSO) test. We performed a leave-one-out analysis to assess the sensitivity of this association. Finally, a meta-analysis of the MR results was undertaken. Results: Our study found a significant positive correlation between TG and SNHL, with OR values of 1.14 (95% CI: 1.07–1.23, p < 0.001) in the IVW analysis and 1.09 (95% CI: 1.03–1.16, p < 0.006) in the replicate analysis. We also found no evidence of horizontal pleiotropy or heterogeneity between the genetic variants (p > 0.05), and a leave-one-out test confirmed the stability and robustness of this association. The meta-analysis combining the initial and replicate analyses showed a significant causal effect with OR values of 1.11 (95% CI: 1.06–1.16, p = 0.01). Conclusion: These findings indicate TG as a risk factor for SNHL, suggesting potential pathways for prevention and intervention in populations at risk. This conclusion underscores the importance of managing TG levels as a strategy to mitigate the risk of developing SNHL. Full article

This study presents a four-objective mathematical model to improve closed-loop supply chain (CLSC) management. The aim of this research is to reduce the costs of the entire chain, risk, emission of pollutants, and time to deliver the product to the customer in uncertain demand condition. In this paper, the NSGAII algorithm is used to solve the model. In this algorithm, among the answers of each generation, a number of them are selected using the two-run tournament selection method. In the binary selection method, the answers are randomly selected from the population, and then a comparison is made between these two answers, and whichever is better is finally selected. The selection criteria in NSGA-II are, firstly, the rank, and secondly, the crowding distance related to the answer. Also, the performance of the NSGA-II algorithm on the same model and data has been compared with the MOPSO algorithm. In the proposed algorithm, if it encounters an impossible solution, it exits the local mode and solves the problem in global conditions. The results show that the proposed method strikes a better balance between discovery and efficiency criteria and avoids falling into local optima. Therefore, in addition to its effectiveness in discovering optimal answers, the genetic-based method has high speed and subsequently, high convergence and diversity rates compared to the particle swarm method. Also, compared to previous methods in the green closed-loop supply chain, the proposed method is better than the modified genetic algorithm, reducing the costs of the chain by about 2.38%. Full article

Color displays have become increasingly attractive, with dielectric optical nanoantennas demonstrating especially promising applications due to the high refractive index of the material, enabling devices to support geometry-dependent Mie resonance in the visible band. Although many structural color designs based on dielectric nanoantennas employ the method of artificial positive adjustment, the design cycle is too lengthy and the approach is non-intelligent. The commonly used phase change material Ge₂Sb₂Te₅ (GST) is characterized by high absorption and a small contrast to the real part of the refractive index in the visible light band, thereby restricting its application in this range. The Sb₂S₃ phase change material is endowed with a wide band gap of 1.7 to 2 eV, demonstrating two orders of magnitude lower propagation loss compared to GST, when integrated onto a silicon waveguide, and exhibiting a maximum refractive index contrast close to 1 at 614 nm. Thus, Sb₂S₃ is a more suitable phase change material than GST for tuning visible light. In this paper, genetic algorithms and finite-difference time-domain (FDTD) solutions are combined and introduced as Sb₂S₃ phase change material to design nanoantennas. Structural color is generated in the reflection mode through the Mie resonance inside the structure, and the properties of Sb₂S₃ in different phase states are utilized to achieve tunability. Compared to traditional methods, genetic algorithms are superior-optimization algorithms that require low computational effort and a high population performance. Furthermore, Sb₂S₃ material can be laser-induced to switch the transitions of the crystallized and amorphous states, achieving reversible color. The large chromatic aberration ∆E modulation of 64.8, 28.1, and 44.1 was, respectively, achieved by the Sb₂S₃ phase transition in this paper. Moreover, based on the sensitivity of the structure to the incident angle, it can also be used in fields such as angle-sensitive detectors. Full article

Uniparental inheritance of mitochondria enables organisms to avoid the costs of intracellular competition among potentially selfish organelles. By preventing recombination, uniparental inheritance may also render a mitochondrial lineage effectively asexual and expose mitochondria to the deleterious effects of Muller’s ratchet. Even among animals and plants, the evolutionary dynamics of mitochondria remain obscure, and less is known about mitochondrial inheritance among fungi. To understand mitochondrial inheritance and test for mitochondrial recombination in one species of filamentous fungus, we took a population genomics approach. We assembled and analyzed 88 mitochondrial genomes from natural populations of the invasive death cap Amanita phalloides, sampling from both California (an invaded range) and Europe (its native range). The mitochondrial genomes clustered into two distinct groups made up of 57 and 31 mushrooms, but both mitochondrial types are geographically widespread. Multiple lines of evidence, including negative correlations between linkage disequilibrium and distances between sites and coalescent analysis, suggest low rates of recombination among the mitochondria (ρ = 3.54 × 10⁻⁴). Recombination requires genetically distinct mitochondria to inhabit a cell, and recombination among A. phalloides mitochondria provides evidence for heteroplasmy as a feature of the death cap life cycle. However, no mushroom houses more than one mitochondrial genome, suggesting that heteroplasmy is rare or transient. Uniparental inheritance emerges as the primary mode of mitochondrial inheritance, even as recombination appears as a strategy to alleviate Muller’s ratchet. Full article